diff --git a/doc/doxygen/DoxygenDumuxLayout.xml b/doc/doxygen/DoxygenDumuxLayout.xml
index 3cfe34c877d9e8546d0bb6917fc5d309eb2dbb60..e9d42835a406e55851c77235a7c7022907aacfd5 100644
--- a/doc/doxygen/DoxygenDumuxLayout.xml
+++ b/doc/doxygen/DoxygenDumuxLayout.xml
@@ -131,7 +131,7 @@
<variables title=""/>
</memberdef>
<includegraph visible="yes"/>
- <includedbygraph visible="yes"/>
+ <includedbygraph visible="no"/>
<authorsection/>
</file>
diff --git a/doc/doxygen/Doxylocal b/doc/doxygen/Doxylocal
index 3dfd4bec026c05ab508b8b2f748c859b3f2428ca..7c2abc2116908d639910132f928d1620c1858b5f 100644
--- a/doc/doxygen/Doxylocal
+++ b/doc/doxygen/Doxylocal
@@ -14,8 +14,8 @@ INPUT += @srcdir@/mainpage.txt \
@srcdir@/modules.txt \
@top_srcdir@/dumux \
@top_srcdir@/test \
- @srcdir@/extradoc/parameterlist.txt \
- @srcdir@/extradoc/featurelist.txt
+ # @srcdir@/extradoc/parameterlist.txt \ # we currently do not have a parameter list. Should be back for 3.1
+ # @srcdir@/extradoc/featurelist.txt # we currently do not have a feature list. Should be back for 3.1
EXAMPLE_PATH += @srcdir@/extradoc
diff --git a/doc/doxygen/customdoxygendumux.css b/doc/doxygen/customdoxygendumux.css
index df09ae1acf454c85e2d3b535801af27e11559061..ad8a591e2929be995fb0689ff12d8098e583e75a 100644
--- a/doc/doxygen/customdoxygendumux.css
+++ b/doc/doxygen/customdoxygendumux.css
@@ -2,6 +2,7 @@
body, table, div, p, dl {
font: 400 14px/22px Roboto,sans-serif;
+ min-width: 500px
}
p.reference, p.definition {
diff --git a/doc/doxygen/modules.txt b/doc/doxygen/modules.txt
index eedaf67e9ab17dbbb5a06789b136a1fbf6390d5f..151586de80ec7b7ddcf29c770ae04b751d706aec 100644
--- a/doc/doxygen/modules.txt
+++ b/doc/doxygen/modules.txt
@@ -375,7 +375,7 @@
*/
/* ***************** Flux ******************/
/*!
- * \defgroup Flux
+ * \defgroup Flux Flux
* \brief All flux related things available in DuMu<sup>x</sup>
*/
/* ***************** Material ******************/
diff --git a/doc/doxygen/sanitizelinks.sh b/doc/doxygen/sanitizelinks.sh
index 3c07e38642e5d47dcfa12633fecafd0990b9284b..76a4079b17e28991a5845e49c5cb76f57ee32790 100755
--- a/doc/doxygen/sanitizelinks.sh
+++ b/doc/doxygen/sanitizelinks.sh
@@ -2,3 +2,6 @@
if [ -e html/modules.html ]; then
sed -i 's/\(init_search();\)/\1 toggleLevel(1);/' html/modules.html
fi
+if [ -e html/modules.HTML ]; then
+ sed -i 's/\(init_search();\)/\1 toggleLevel(1);/' html/modules.HTML
+fi
diff --git a/doc/handbook/dumux-handbook.bib b/doc/handbook/dumux-handbook.bib
index 4e61894b70634f753934f53935d74bc45eec32a1..4ea2fe68427f72273c3fd379acb35dd5807b71fd 100644
--- a/doc/handbook/dumux-handbook.bib
+++ b/doc/handbook/dumux-handbook.bib
@@ -464,6 +464,29 @@
url={https://dx.doi.org/10.1021/jp021943g}
}
+@article{witherspoon1965,
+author = {Witherspoon, P. A. and Saraf, D. N.},
+title = {{Diffusion of Methane, Ethane, Propane, and n-Butane in Water from 25 to 43°}},
+journal = {The Journal of Physical Chemistry},
+volume = {69},
+number = {11},
+pages = {3752--3755},
+year = {1965},
+doi = {10.1021/j100895a017},
+url = {https://doi.org/10.1021/j100895a017},
+}
+
+@article{han2003,
+ title={{Description of fluid flow around a wellbore with stress-dependent porosity and permeability}},
+ author={Han, Gang and Dusseault, Maurice B},
+ journal={Journal of Petroleum science and engineering},
+ volume={40},
+ number={1-2},
+ pages={1--16},
+ year={2003},
+ publisher={Elsevier}
+}
+
@INPROCEEDINGS{A3:aavatsmark:1994,
author = {Aavatsmark, I. and Barkve, T. and B{\o}e, {\O}. and Mannseth, T.},
title = {{Discretization on non-orthogonal, curvilinear grids for multiphase
@@ -1715,6 +1738,19 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
url = {https://doi.org/10.2514/1.36541}
}
+@Article{launder1974a,
+author = {B.E. Launder and B.I. Sharma},
+title = {{Application of the energy-dissipation model of turbulence to the calculation of flow near a spinning disc}},
+journal = {Letters in Heat and Mass Transfer},
+volume = {1},
+number = {2},
+pages = {131 -- 137},
+year = {1974},
+issn = {0094--4548},
+doi = {https://doi.org/10.1016/0094-4548(74)90150-7},
+url = {http://www.sciencedirect.com/science/article/pii/0094454874901507},
+}
+
@Book{Versteeg2009a,
title = {{An Introduction to Computational Fluid Dynamics}},
publisher = {Pearson Education},
diff --git a/dumux/discretization/cellcentered/elementsolution.hh b/dumux/discretization/cellcentered/elementsolution.hh
index 47dc7b7e026da179ceb486f56e5bb09233e1d410..892ffe0c818009ba12356836fbfb9365a8734212 100644
--- a/dumux/discretization/cellcentered/elementsolution.hh
+++ b/dumux/discretization/cellcentered/elementsolution.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief The local element solution class for cell-centered methods
*/
#ifndef DUMUX_CC_ELEMENT_SOLUTION_HH
@@ -32,7 +32,7 @@
namespace Dumux {
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief The element solution vector
*/
template<class FVElementGeometry, class PV>
@@ -106,7 +106,7 @@ private:
};
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
*/
template<class Element, class SolutionVector, class FVGridGeometry>
@@ -122,7 +122,7 @@ auto elementSolution(const Element& element, const SolutionVector& sol, const FV
}
/*!
-* \ingroup CCDiscretization
+* \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
*/
template<class Element, class ElementVolumeVariables, class FVElementGeometry>
@@ -136,7 +136,7 @@ auto elementSolution(const Element& element, const ElementVolumeVariables& elemV
}
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
* \note This is e.g. used to contruct an element solution at Dirichlet boundaries
*/
@@ -150,7 +150,7 @@ auto elementSolution(PrimaryVariables&& priVars)
}
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
* \note This is e.g. used to contruct an element solution at Dirichlet boundaries
*/
diff --git a/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh b/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
index 483bcc0eccc25f7b4644a6a6c8ff8b672b1297cc..f1fe3f285220bd08555941e4f1e88ea44a437329 100644
--- a/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
+++ b/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
@@ -73,6 +73,7 @@ namespace CCMpfa {
* \param volVars The container where the volume variables are stored
* \param volVarIndices The container where the volume variable indices are stored
* \param problem The problem containing the Dirichlet boundary conditions
+ * \param element The element to which the finite volume geometry is bound
* \param fvGeometry The element finite volume geometry
* \param nodalIndexSet The dual grid index set around a node
*/
diff --git a/dumux/discretization/staggered/elementsolution.hh b/dumux/discretization/staggered/elementsolution.hh
index 846c94adcd15c4cd1f69512b9e568223a1b2aeb4..140c38b24ebd734c6af2424c2b2029e838c04403 100644
--- a/dumux/discretization/staggered/elementsolution.hh
+++ b/dumux/discretization/staggered/elementsolution.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief The local element solution class for staggered methods
*/
#ifndef DUMUX_STAGGERED_ELEMENT_SOLUTION_HH
@@ -31,7 +31,7 @@
namespace Dumux {
/*!
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief Helper function to create a PrimaryVariables object from CellCenterPrimaryVariables
* \tparam PrimaryVariables The type of the desired primary variables object
* \tparam CellCenterPrimaryVariables The type of the cell center (input) primary variables object
@@ -54,7 +54,7 @@ template<class PrimaryVariables>
using StaggeredElementSolution = Dune::BlockVector<PrimaryVariables>;
/*!
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for staggered schemes
* \note This is e.g. used to construct an element solution at Dirichlet boundaries
*/
@@ -67,7 +67,7 @@ auto elementSolution(PrimaryVariables&& priVars)
}
/*!
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief Helper function to create an elementSolution from cell center primary variables
* \tparam PrimaryVariables The type of the desired primary variables object
* \tparam CellCenterPrimaryVariables The type of the cell center (input) primary variables object
diff --git a/dumux/freeflow/navierstokes/iofields.hh b/dumux/freeflow/navierstokes/iofields.hh
index b38b8f5a07b566ad3faf9dfd0ffb3f7c0d1b0d38..e50a4199694e2f1d835edb82b0dbcb1926138bdf 100644
--- a/dumux/freeflow/navierstokes/iofields.hh
+++ b/dumux/freeflow/navierstokes/iofields.hh
@@ -37,7 +37,6 @@ namespace Dumux
{
/*!
- * \ingroup InputOutput
* \ingroup NavierStokesModel
* \brief helper function to determine the names of cell-centered primary variables of a model with staggered grid discretization
* \note use this as input for the load solution function
@@ -58,7 +57,6 @@ std::function<std::string(int,int)> createCellCenterPVNameFunction(const std::st
}
/*!
- * \ingroup InputOutput
* \ingroup NavierStokesModel
* \brief helper function to determine the names of primary variables on the cell faces of a model with staggered grid discretization
* \note use this as input for the load solution function
diff --git a/dumux/freeflow/rans/twoeq/kepsilon/model.hh b/dumux/freeflow/rans/twoeq/kepsilon/model.hh
index bd94bd8329dc24f906cda1d91f20355d362d489d..2eabe5fed4cd7e8fbcff4b4b9e9a916c4f14b57b 100644
--- a/dumux/freeflow/rans/twoeq/kepsilon/model.hh
+++ b/dumux/freeflow/rans/twoeq/kepsilon/model.hh
@@ -26,7 +26,8 @@
*
* The k-epsilon models calculate the eddy viscosity with two additional PDEs,
* one for the turbulent kinetic energy (k) and for the dissipation (\f$ \varepsilon \f$).
- * The model uses the one proposed by Launder and Sharma \cite{Launder1994a}.
+ * The model uses the one proposed by Launder and Sharma \cite launder1974a
+ * https://doi.org/10.1016/0094-4548(74)90150-7.
*
* The turbulent kinetic energy balance is:
* \f[
diff --git a/dumux/linear/seqsolverbackend.hh b/dumux/linear/seqsolverbackend.hh
index fa408d4ff054efa5fd6cf3e31feee0bacb8d23a7..70bdd880c3ed022d2a007d72de7a97fe57d13c35 100644
--- a/dumux/linear/seqsolverbackend.hh
+++ b/dumux/linear/seqsolverbackend.hh
@@ -831,7 +831,7 @@ private:
*/
// \{
-/*
+/*!
* A simple ilu0 block diagonal preconditioner
*/
template<class M, class X, class Y, int blockLevel = 2>
@@ -875,17 +875,8 @@ public:
static_assert(blockLevel >= 2, "Only makes sense for MultiTypeBlockMatrix!");
}
- /*!
- \brief Prepare the preconditioner.
-
- \copydoc Dune::Preconditioner::pre(X&,Y&)
- */
void pre (X& v, Y& d) final {}
- /*!
- * \brief Apply the preconditoner.
- * \copydoc Dune::Preconditioner::apply(X&,const Y&)
- */
void apply (X& v, const Y& d) final
{
using namespace Dune::Hybrid;
@@ -895,10 +886,6 @@ public:
});
}
- /*!
- * \brief Clean up.
- * \copydoc Dune::Preconditioner::post(X&)
- */
void post (X&) final {}
//! Category of the preconditioner (see SolverCategory::Category)
@@ -1006,9 +993,20 @@ public:
}
/*!
- \brief Prepare the preconditioner.
-
- \copydoc Dune::Preconditioner::pre(X&,Y&)
+ * \brief Prepare the preconditioner.
+ *
+ * A solver solves a linear operator equation A(v)=d by applying
+ * one or several steps of the preconditioner. The method pre()
+ * is called before the first apply operation.
+ * d and v are right hand side and solution vector of the linear
+ * system respectively. It may. e.g., scale the system, allocate memory or
+ * compute a (I)LU decomposition.
+ * Note: The ILU decomposition could also be computed in the constructor
+ * or with a separate method of the derived method if several
+ * linear systems with the same matrix are to be solved.
+ *
+ * \param v The left hand side of the equation.
+ * \param d The right hand side of the equation.
*/
void pre (X& v, Y& d) final
{
@@ -1020,8 +1018,15 @@ public:
}
/*!
- * \brief Apply the preconditoner.
- * \copydoc Dune::Preconditioner::apply(X&,const Y&)
+ * \brief Apply one step of the preconditioner to the system A(v)=d.
+ *
+ * On entry v=0 and d=b-A(x) (although this might not be
+ * computed in that way. On exit v contains the update, i.e
+ * one step computes \f$ v = M^{-1} d \f$ where \f$ M \f$ is the
+ * approximate inverse of the operator \f$ A \f$ characterizing
+ * the preconditioner.
+ * \param v The update to be computed
+ * \param d The current defect.
*/
void apply (X& v, const Y& d) final
{
@@ -1034,7 +1039,12 @@ public:
/*!
* \brief Clean up.
- * \copydoc Dune::Preconditioner::post(X&)
+ *
+ * This method is called after the last apply call for the
+ * linear system to be solved. Memory may be deallocated safely
+ * here. v is the solution of the linear equation.
+ *
+ * \param v The right hand side of the equation.
*/
void post (X& v) final
{
diff --git a/dumux/material/binarycoefficients/h2o_ch4.hh b/dumux/material/binarycoefficients/h2o_ch4.hh
index c90f35ad8a6d5ac833fba5fd2814b97c45f50683..c7c5d63803df2cc26133d13ca21e68d6bcef3c0d 100644
--- a/dumux/material/binarycoefficients/h2o_ch4.hh
+++ b/dumux/material/binarycoefficients/h2o_ch4.hh
@@ -96,8 +96,8 @@ public:
* linear dependency on temperature. We thus simply scale the
* experimentally obtained diffusion coefficient of Ferrell and
* Himmelblau by the temperature.<br>
- * This function use an interpolation of the data by \cite{Whitherspoon1965}
- * \url{http://dx.doi.org/10.1021/j100895a017}
+ * This function use an interpolation of the data by \cite witherspoon1965
+ * http://dx.doi.org/10.1021/j100895a017
*/
template <class Scalar>
static Scalar liquidDiffCoeff(Scalar temperature, Scalar pressure)
diff --git a/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh b/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
index 049d7b57bafa06fde5adbbb213540ed19a0b328d..0a75f5149e4ca5477601b6921f6c5e6ddf93a185 100644
--- a/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
+++ b/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
@@ -61,7 +61,7 @@ public:
* \param values Container for the return values
* \param params Array of Parameters
* \param state The fluid state
- * \param wPhaseIdx the phase index of the wetting phase
+ * \param wPhaseIdx The phase index of the wetting phase
*/
template <class ContainerT, class FluidState>
static void capillaryPressures(ContainerT &values,
@@ -82,6 +82,7 @@ public:
* \param values Container for the return values
* \param params Array of Parameters
* \param state The fluid state
+ * \param wPhaseIdx the phase index of the wetting phase
*/
template <class ContainerT, class FluidState>
static void relativePermeabilities(ContainerT &values,
diff --git a/dumux/material/fluidmatrixinteractions/porositydeformation.hh b/dumux/material/fluidmatrixinteractions/porositydeformation.hh
index c40c61d3dec854e953041b0f9eefde1cff1be16a..3e0001a0721217739881a7f3b5779ca16a36f8d5 100644
--- a/dumux/material/fluidmatrixinteractions/porositydeformation.hh
+++ b/dumux/material/fluidmatrixinteractions/porositydeformation.hh
@@ -44,7 +44,6 @@ public:
* the displacements in the different grid directions are stored
* in the first entries of the primary variable vector.
*
- *
* \param fvGridGeometry The finite volume grid geometry
* \param element The finite element
* \param elemSol The element solution
@@ -53,10 +52,10 @@ public:
* \param minPoro A minimum porosity value
* \param maxPoro A maximum porosity value
*
- * \note Han and Dusseault (2003, doi 10.1016/S0920-4105(03)00047-0)
- * provide a derivation for \f$\text{d} \phi = -(1 - \phi ) \text{d} \epsilon_v\f$.
- * Here, \f$\epsilon_v\f$ is equal to \f$text{div} \mathbf{u}\f$.
- * By using an initial porosity \f$\phi_0\f$ and assuming \epsilon_{v, 0} = 0,
+ * \note \cite han2003 ( https://doi.org/10.1016/S0920-4105(03)00047-0 )
+ * provide a derivation for \f$\text{d} \phi = -(1 - \phi ) \text{d} \epsilon_v \f$.
+ * Here, \f$\epsilon_v\f$ is equal to \f$\text{div} \mathbf{u}\f$.
+ * By using an initial porosity \f$\phi_0\f$ and assuming \f$ \epsilon_{v, 0} = 0 \f$,
* one obtains \f$\phi = \frac{\phi_0 - \text{div} \mathbf{u}}{1 - \text{div} \mathbf{u}}\f$,
* which is the formulation for the rock mechanics sign convention. Here we are
* using the continuum mechanics sign convention, thus, the final formula reads:
diff --git a/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh b/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
index 09f7a680db0a3fd983db9294ad7039d254c141c2..0272454a15e2724cc649ec42f70d148db087ae44 100644
--- a/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
+++ b/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
@@ -91,7 +91,6 @@ public:
int idx1, int idx2, int idx3, int idx4, int idx5, int idx6,
Dune::FieldVector<bool, 4> &useCases);
-
int transmissibilityTPFA(Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
@@ -120,7 +119,6 @@ public:
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx6);
-
/*!
* \brief Constructs a FvMpfaL3dTransmissibilityCalculator object
* \param problem A problem class object
diff --git a/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh b/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
index 0606c2bf86a7118ea591e52d39b591388962b93a..cb45b31911f25b6c15f67c85e3b1cc1b8a6b8ae5 100644
--- a/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
+++ b/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
@@ -255,8 +255,6 @@ public:
* potentially solution dependent and requires some quantities that
* are specific to the fully-implicit method.
*
- * \param values The neumann values for the conservation equations in units of
- * \f$ [ \textnormal{unit of conserved quantity} / (m^2 \cdot s )] \f$
* \param element The finite element
* \param fvGeometry The finite-volume geometry
* \param elemVolVars All volume variables for the element
@@ -267,9 +265,9 @@ public:
* E.g. for the mass balance that would the mass flux in \f$ [ kg / (m^2 \cdot s)] \f$.
*/
NumEqVector neumann(const Element& element,
- const FVElementGeometry& fvGeometry,
- const ElementVolumeVariables& elemVolVars,
- const SubControlVolumeFace& scvf) const
+ const FVElementGeometry& fvGeometry,
+ const ElementVolumeVariables& elemVolVars,
+ const SubControlVolumeFace& scvf) const
{
return NumEqVector(0.0);
}